Polycomb Associates Genome-wide with a Specific RNA Polymerase II Variant,and Regulates Metabolic Genes in ESCs

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Highlights? A unique RNAPII variant (S5p⁺S7p^?S2p^?) binds PRC targets genome-wide in ESCs ? RNAPII-S5p and PRC coincide in time and localization, and show proportional abundance ? Novel, active PRC-target genes identified in ESCs include metabolic genes ? Active PRC targets switch between on/off (active/PRC) states in the ESC population     

The challenges of cellular compartmentalization in plant metabolic engineering

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Highlights► Targeting enzymes to organelles with highest precursor pool affects product yield. ► Targeting of nonendogenous enzymes to organelles is a useful tool for engineering. ► Identification of transporters is central for effective metabolic engineering. ► Advances in metabolomics of isolated organelles will impact engineering strategies. ► Future plant metabolic engineering will include introduction of entire pathways.     

Recent progress in the metabolic engineering of alkaloids in plant systems

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Highlights► Recent metabolic engineering efforts for plant alkaloids. ► Characterizing, reconfiguring and fine-tuning metabolic ‘parts’ improves titers. ► Additional strategies are necessary to produce ‘unnatural’ natural products.     

Thermoacidophilic Sulfolobus species as source for extremozymes and as novel archaeal platform organisms

Sulfolobus species – thermoacidophilic Archaea – as sources for novel extremozymes and as novel platform organism for metabolic engineering and synthetic biology.

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Comparative genomics approaches to understanding and manipulating plant metabolism

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Highlights► Comparative genomics can help predict the function of unknown plant metabolic genes. ► Functional gene annotations are foundational to the construction of metabolic models. ► Models can simulate effects of genetic changes and thus guide metabolic engineering. ► Examples of comparative genomics facilitating gene discovery in plants are presented.     

Conformational dynamics of activation for the pentameric complex of dimeric G protein-coupled receptor and heterotrimeric G protein

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Highlights? Dynamics of dimeric Rho complexes in three different conformational states examined ? Photoactivation of Rho (Rho¹) causes structural relaxation of the helical bundle ? Binding of Gt to Rho¹ reduces flexibility of Rho¹ but increases flexibility in Gt ? Free Rho¹ exhibits different a conformation than it does in the Rho¹-G_t complex     

Adipose Vascular Endothelial Growth Factor Regulates Metabolic Homeostasis through Angiogenesis

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Highlights? Two-way modulations of adipose VEGF were generated with aP2-Cre transgene ? Adipose VEGF KO reduces vasculature, increases hypoxia and inflammation in fat ? Adipose VEGF KO accelerates the development of metabolic disease in high-fat diet ? Induced adipose VEGF has opposite effect on fat and restores metabolic homeostasis     

Profiling metabolic networks to study cancer metabolism

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Highlights► Metabolic dependencies that arise in tumors may present new opportunities for therapy. ► Advanced methods in metabolic systems biology can help identify these dependencies. ► Application of isotope tracers to cancer models can facilitates quantitation of fluxes. ► Tumors with compromised TCA metabolism exhibit unique metabolic profiles.     

Transcriptome data modeling for targeted plant metabolic engineering

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Highlights► Network analysis is essential for data mining of omics-based large-scale data sets. ► Gene coexpression analysis is useful for prediction of gene function. ► Comparative network analysis can reveal common and unique plant metabolic pathways. ► Novel genome editing tools facilitate rational metabolic engineering.     

Stable isotope-assisted metabolomics to detect metabolic flux changes in mammalian cell cultures

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Highlights► Stable isotope-assisted metabolomics is powerful to determine metabolic fluxes. ► Stable isotope-assisted metabolomics is more complex for mammalian cell cultures. ► Biotechnological processes can be improved by assessing metabolic flux changes. ► Metabolic flux analysis is an attractive tool for toxicity studies. ► There is a huge potential for future applications on mammalian systems.     

Metabolic network flux analysis for engineering plant systems

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Highlights► A powerful range of tools has been developed for metabolic network flux analysis. ► These tools yield insights that are used to aid microbial metabolic engineering. ► Plants present great opportunities and special challenges to applying these tools. ► Tool selection and knowledge of plant systems is key to practical success.     

Cathepsin L Regulates Metabolic Networks Controlling Rapid Cell Growth and Proliferation

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Highlights

• •Cts L^−/− cells proliferate faster than wild types and shift to aerobic glycolysis.
• •LDHA is a key glycolytic enzyme controlling Cts L^−/− cell proliferation.
• •Cts L regulates LDHA expression and function.

     

Streamlining genomes: toward the generation of simplified and stabilized microbial systems

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Highlights? Top-down and bottom-up approaches to genome streamlining. ? Computational support for constructing and refactoring streamlined genomes. ? From genome engineering to metabolic reprogramming. ? Perspectives in applied genome engineering.     

Metabolomics platforms for genome wide association studies—linking the genome to the metabolome

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Highlights► Genome-wide association studies with metabolomics constitute mGWAS. ► mGWAS provide insights into genetic and environmental impact on metabolic processes. ► We review essential strategies for mGWAS. ► Examples of mGWAS in large cohort studies are discussed.     

A three-state model of telomere control over human proliferative boundaries

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Highlights? Human telomeres are protected from the DDR by a higher-order structure. ? Intermediate-state telomeres are susceptible to a DDR and regulate senescence. ? Uncapped-state telomeres are susceptible to fusions and induce crisis. ? Intermediate-state telomeres regulate the prolonged mitosis checkpoint. ? Telomeres may serve as epigenetic sensors of cellular stress.     

Metabolic Cross-talk Between Human Bronchial Epithelial Cells and Internalized Staphylococcus aureus as a Driver for Infection*

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Highlights

• •Interplay of epithelial cells and internalized S. aureus was dissected over 96 h.
• •Surviving host cells contain nonreplicating bacteria that persists in the cytoplasm.
• •Competition over resources triggers temporal metabolic changes.
• •Metabolic adaptation of host and bacteria determines the outcome of infection.

     

Integrated Succinylome and Metabolome Profiling Reveals Crucial Role of S-Ribosylhomocysteine Lyase in Quorum Sensing and Metabolism of Aeromonas hydrophila,

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Highlights

• •A global lysine succinylome was investigated in A. hydrophila.
• •The lysine succinylation modifications play crucial role on various metabolic pathways.
• •Reversible succinylation on Lys23 and Lys30 regulates the activity of S-ribosylhomocysteine lyase LuxS.
• •Lysine succinylation modifications of LuxS affect quorum sensing and metabolism.

     

N-terminal Acetylation Levels Are Maintained During Acetyl-CoA Deficiency in Saccharomyces cerevisiae

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Highlights

• •First global study on metabolic regulation of Nt-acetylation.
• •Yeast cells maintain global Nt-acetylation levels during prolonged starvation.
• •Nt-acetylation can in some cases be either up- or downregulated by starvation.
• •Naa10/NatA affects the steady-state protein levels of Rsa3 and Rpl7a.

     

ADF/cofilin regulates secretory cargo sorting at the TGN via the Ca2+ ATPase SPCA1

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Highlights? ADF/cofilin localizes to the TGN and binds SPCA1 in an actin-dependent manner ? Dynamic actin regulates the activity of the Ca²⁺ pump SPCA1 ? ADF/cofilin facilitates secretory cargo sorting in a Ca²⁺-dependent manner